Wha does combineGVCFs does to loci with variant only in gVCF from another analysis?
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13 months ago

I called variants on two batches, each 3 samples. I want to merge those two batches with combineGVCFs, but i don't understand what happens to variant positions that were not present in one of the batches. Is it removed? Is it replaced with reference?

gatk • 436 views
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